Ailong Ke
Eugene Higgins Professor of Molecular Biophysics and BiochemistryCards
About
Research
Publications
2025
Conversion of IscB and Cas9 into RNA-guided RNA editors
Xu C, Niu X, Sun H, Yan H, Tang W, Ke A. Conversion of IscB and Cas9 into RNA-guided RNA editors. Cell 2025, 188: 5847-5861.e11. PMID: 40829585, PMCID: PMC12798835, DOI: 10.1016/j.cell.2025.07.032.Peer-Reviewed Original ResearchConceptsEvolutionary ancestorA-to-I editingDouble-stranded DNA binding activityHuman cellsRNA-targeting toolsRNA cleavage activityDNA binding activitySingle-stranded (ss)DNASplicing outcomesRNA 2RNA editingTrans-splicingRNA editorsCRISPR-Cas13Motif domainDNA editingCleavage activityBinding activityMRNA knockdownCas9Cas13Intrinsic affinityUndesired cytotoxicityRNAMRNA levelsEscherichia coli yybP-ykoY Riboswitch as a Tandem Riboswitch Regulated by Mn2+ and pH
Xiao W, Liu G, Chen T, Zhang Y, Ke A, Cai R, Lu C. Escherichia coli yybP-ykoY Riboswitch as a Tandem Riboswitch Regulated by Mn2+ and pH. ACS Chemical Biology 2025, 20: 1010-1019. PMID: 40252020, PMCID: PMC12951517, DOI: 10.1021/acschembio.4c00715.Peer-Reviewed Original ResearchConceptsAptamer domainControl of gene expressionAdaptive responses to environmental changeGene expressionResponse to environmental changesYybP-ykoY riboswitchBind Mg2+Combination of crystallographySignificant conformational changesThree-way junctionRiboswitch aptamer domainTandem domainsTandem riboswitchRiboswitchTranslational levelTertiary structureRegulatory mechanismsPocket-like structureConformational changesConformational dynamicsEnvironmental changesChemical probesSHAPE probingSmall-angle X-ray scatteringAptamer
2024
Assessing and engineering the IscB–ωRNA system for programmed genome editing
Yan H, Tan X, Zou S, Sun Y, Ke A, Tang W. Assessing and engineering the IscB–ωRNA system for programmed genome editing. Nature Chemical Biology 2024, 20: 1617-1628. PMID: 38977787, PMCID: PMC12213078, DOI: 10.1038/s41589-024-01669-3.Peer-Reviewed Original ResearchConceptsGenome editingHuman genomeEvolutionary ancestorIn vitro DNA binding affinityHuman cellsAmino acid substitutionsDNA binding affinityIn vivo genome editingR-loopsAcid substitutionsWild-typeGenomeTarget siteCas9IndelsOff-target profilesCellsNucleotideMotifHuman genome editingTarget selectionAminoModerate fidelityExploiting activation and inactivation mechanisms in type I-C CRISPR-Cas3 for genome-editing applications
Hu C, Myers M, Zhou X, Hou Z, Lozen M, Nam K, Zhang Y, Ke A. Exploiting activation and inactivation mechanisms in type I-C CRISPR-Cas3 for genome-editing applications. Molecular Cell 2024, 84: 463-475.e5. PMID: 38242128, PMCID: PMC10857747, DOI: 10.1016/j.molcel.2023.12.034.Peer-Reviewed Original ResearchConceptsNon-target DNA strandType I CRISPR-Cas systemsEukaryotic genome engineeringHuman cellsAnti-CRISPR proteinsGenome-editing applicationsCRISPR-Cas3Anti-CRISPRNuclease-helicaseType I-CGenome engineeringGenomic deletionsPAM recognitionDNA bindingTranscriptional modulationBinding grooveDNA targetsGenome editingDNA strandsAllosteric inhibitionCascade complexGenomeCas3Cleavage mechanismOff-switch
2023
Multiple adaptations underly co-option of a CRISPR surveillance complex for RNA-guided DNA transposition
Park J, Petassi M, Hsieh S, Mehrotra E, Schuler G, Budhathoki J, Truong V, Thyme S, Ke A, Kellogg E, Peters J. Multiple adaptations underly co-option of a CRISPR surveillance complex for RNA-guided DNA transposition. Molecular Cell 2023, 83: 1827-1838.e6. PMID: 37267904, PMCID: PMC10693918, DOI: 10.1016/j.molcel.2023.05.005.Peer-Reviewed Original ResearchConceptsCRISPR-associated transposonsRNA-guided DNA transpositionCRISPR-CasDNA transpositionSurveillance complexDNA-targeting modulesR-loop formationCRISPR-Cas systemsAttachment sitesEffector complexesR-loopsCRISPR RNAPAM sequenceSequence requirementsTransposition systemSequence driftCrRNA targetsTniQAmino acidsTransposonCrRNAHost surveillanceMultiple adaptationsSequenceCo-option
2022
Craspase is a CRISPR RNA-guided, RNA-activated protease
Hu C, van Beljouw S, Nam K, Schuler G, Ding F, Cui Y, Rodríguez-Molina A, Haagsma A, Valk M, Pabst M, Brouns S, Ke A. Craspase is a CRISPR RNA-guided, RNA-activated protease. Science 2022, 377: 1278-1285. PMID: 36007061, PMCID: PMC10041820, DOI: 10.1126/science.add5064.Peer-Reviewed Original ResearchConceptsTarget RNA cleavageRNA cleavageCaspase-like proteinsCRISPR-guided caspaseSide-chain binding pocketProtospacer flanking sequenceEndogenous protein substratesRNA-guidedFlanking sequencesProtein substratesCraspaseCRISPR-CasCatalytic dyadRNA targetsProtease activityGate loopProteaseRNAActivation mechanismSite-specificCleavageProtospacerGRAMPSCaspaseCRISPRAllosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools
Hu C, Ni D, Nam K, Majumdar S, McLean J, Stahlberg H, Terns M, Ke A. Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools. Molecular Cell 2022, 82: 2754-2768.e5. PMID: 35835111, PMCID: PMC9357151, DOI: 10.1016/j.molcel.2022.06.007.Peer-Reviewed Original ResearchConceptsEffector complexesAllele-specific inactivationHD nucleaseAllosteric controlType I CRISPR-Cas systemsR-loop formationRNA-guided complexesNucleic acid detection toolsDisease-causing mutationsGenome editing toolsCRISPR-Cas3R-loopsRNA-guidedDNA recognitionDNA degradationDNA targetsCas3Nucleic acid detectionCryoelectron microscopyHuman cellsCryo-EMEditing toolsAcid detectionTarget regionPyrococcusStructural basis for RNA-guided DNA cleavage by IscB-ωRNA and mechanistic comparison with Cas9
Schuler G, Hu C, Ke A. Structural basis for RNA-guided DNA cleavage by IscB-ωRNA and mechanistic comparison with Cas9. Science 2022, 376: 1476-1481. PMID: 35617371, PMCID: PMC10041819, DOI: 10.1126/science.abq7220.Peer-Reviewed Original ResearchConceptsRNA-guided DNA cleavageCryo-electron microscopy structureDouble-stranded DNADNA cleavageR-loop formationDouble-stranded DNA targetsRNA-DNA heteroduplexDNA cleavage mechanismREC domainR-loopsCRISPR RNADomain organizationMotif recognitionRNA-DNADomain replacementStructural basisCas9Cryo-electronCas9 ribonucleoproteinCleavage mechanismDNACleavageIS200/IS605TransposonCas12tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-Box Riboswitch
Grigg J, Price I, Ke A. tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-Box Riboswitch. Crystals 2022, 12: 694. DOI: 10.3390/cryst12050694.Peer-Reviewed Original ResearchT-boxLow-resolution crystal structureTRNA anticodon armT-box riboswitchesRNA structure determinationTarget RNA moleculesStructure determinationAnticodon armCo-crystal structureTRNAProbability of crystallizationRNA moleculesRiboswitch systemAntiterminationOpen conformationStructural snapshotsRNACrystal packingNMR studiesCrystal structureSensing mechanismProheadRiboswitchAminoacylationMisfoldingReconstitution and biochemical characterization of the RNA-guided helicase-nuclease protein Cas3 from type I-A CRISPR–Cas system
Hu C, Ke A. Reconstitution and biochemical characterization of the RNA-guided helicase-nuclease protein Cas3 from type I-A CRISPR–Cas system. Methods In Enzymology 2022, 673: 405-424. PMID: 35965014, DOI: 10.1016/bs.mie.2022.03.059.Peer-Reviewed Original Research
Academic Achievements & Community Involvement
News
Get In Touch
Contacts
Email
Academic Office Number